X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=98510e39524e0b415780f424ca6f323ba53ca583;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=0f51b7e538b9c3c25e7d397f7df51fb21d072e61;hpb=985fd5ff517f3eb5221a7aefec88138341514779;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 0f51b7e..98510e3 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -125,8 +125,7 @@ public class Alignment implements AlignmentI
   /**
    * Make a new alignment from an array of SeqCigars
    * 
-   * @param seqs
-   *          SeqCigar[]
+   * @param alseqs
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -195,6 +194,7 @@ public class Alignment implements AlignmentI
   {
     synchronized (sequences)
     {
+    
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -398,6 +398,10 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+  private ArrayList<SequenceGroup> temp = new ArrayList<>();
+
   /*
    * (non-Javadoc)
    * 
@@ -407,11 +411,15 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
       int gSize = groups.size();
+      if (gSize == 0)
+      {
+        return noGroups;
+      }
+      temp.clear();
       for (int i = 0; i < gSize; i++)
       {
         SequenceGroup sg = groups.get(i);
@@ -589,11 +597,12 @@ public class Alignment implements AlignmentI
     int i = 0;
     SequenceI sq = null;
     String sqname = null;
+    int nseq = sequences.size();
     if (startAfter != null)
     {
       // try to find the sequence in the alignment
       boolean matched = false;
-      while (i < sequences.size())
+      while (i < nseq)
       {
         if (getSequenceAt(i++) == startAfter)
         {
@@ -606,7 +615,7 @@ public class Alignment implements AlignmentI
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
@@ -712,12 +721,8 @@ public class Alignment implements AlignmentI
   
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() > maxLength)
-      {
-        maxLength = getSequenceAt(i).getLength();
-      }
+      maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
     }
-  
     return maxLength;
   }
 
@@ -1192,7 +1197,8 @@ public class Alignment implements AlignmentI
     int maxLength = -1;
 
     SequenceI current;
-    for (int i = 0; i < sequences.size(); i++)
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
@@ -1209,7 +1215,7 @@ public class Alignment implements AlignmentI
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
@@ -2028,4 +2034,17 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void resetColors()
+  {
+    for (int i = getHeight(); --i >= 0;)
+    {
+      sequences.get(i).resetColors();
+    }
+    // if (dataset != null)
+    // {
+    // dataset.resetColors();
+    // }
+  }
+
 }